Hmmm, you have some point, but I think you overstate the case. I agree that there are certain philosophical prerequisites (logic, a few premises that you can check for self-consistency but not otherwise validate empirically) required for science.

But the embryo is not-an-individual not by virtue of ontology in the abstract, but because of detailed studies of the physical nature of embryos that show that the qualities that we associate with individuals are not possessed by embryos. It is no different ontologically than an argument that bats are not birds: we could argue that linguistically we could group them with one term, but not that "bat" is what we mean by "bird" when birds are a monophyletic group that excludes, say, sheep.

There are always epistemological issues about our beliefs, but that is true about any matter of fact.